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CHECK report for Rsamtools on malbec2

This page was generated on 2020-10-17 11:55:38 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Rsamtools PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1539/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rsamtools 2.4.0
Bioconductor Package Maintainer
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/Rsamtools
Branch: RELEASE_3_11
Last Commit: 3871cc8
Last Changed Date: 2020-04-27 14:21:43 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rsamtools
Version: 2.4.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Rsamtools.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Rsamtools_2.4.0.tar.gz
StartedAt: 2020-10-17 05:01:51 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:04:41 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 170.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: Rsamtools.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:Rsamtools.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings Rsamtools_2.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/Rsamtools.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rsamtools/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rsamtools’ version ‘2.4.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Rsamtools’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
  bamfile.c:168:13: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
  /home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
  tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
See ‘/home/biocbuild/bbs-3.11-bioc/meat/Rsamtools.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  9.8Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      5.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Versioned 'LinkingTo' value for ‘Rhtslib’ is only usable in R >= 3.0.2
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘S4Vectors:::explodeIntBits’ ‘S4Vectors:::implodeIntBits’
  ‘S4Vectors:::makePowersOfTwo’ ‘S4Vectors:::quick_unlist’
  ‘S4Vectors:::selectSome’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.11-bioc/R/library/Rsamtools/libs/Rsamtools.so’:
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘abort’, possibly from ‘abort’ (C)
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘srand48’, possibly from ‘srand48’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
         user system elapsed
pileup 38.275  0.104  38.383
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘Rsamtools_unit_tests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/Rsamtools.Rcheck/00check.log’
for details.

Installation output

Rsamtools.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL Rsamtools
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PosCacheColl.cpp -o PosCacheColl.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ResultManager.cpp -o ResultManager.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c as_bam.c -o as_bam.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam.c -o bam.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_data.c -o bam_data.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_mate_iter.cpp -o bam_mate_iter.o
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/sam.h:29:0,
                 from Template.h:9,
                 from BamIterator.h:10,
                 from BamRangeIterator.h:7,
                 from bam_mate_iter.cpp:2:
BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ~~~~~~~~~^~~~~~~~~~~~~~
BamRangeIterator.h:138:9: note: in expansion of macro ‘bam_seek’
         bam_seek(bfile, pos, SEEK_SET);
         ^~~~~~~~
BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/bam.h:57:41: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ~~~~~~~~~^~~~~~~~~~~~~~
BamIterator.h:87:9: note: in expansion of macro ‘bam_seek’
         bam_seek(bfile, 0, 0);
         ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bam_sort.c -o bam_sort.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bambuffer.c -o bambuffer.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bamfile.c -o bamfile.o
bamfile.c: In function ‘bamfile_isincomplete’:
bamfile.c:168:13: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
             bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c: In function ‘bamfile_open’:
bamfile.c:29:15: warning: ‘cfile’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         index = hts_idx_load2(file, indexname);
         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bamfile.c:73:17: note: ‘cfile’ was declared here
     const char *cfile;
                 ^~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c bcffile.c -o bcffile.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c encode.c -o encode.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fafile.c -o fafile.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c idxstats.c -o idxstats.o
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/sam.h:29:0,
                 from bamfile.h:5,
                 from idxstats.c:1:
idxstats.c: In function ‘idxstats_bamfile’:
/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:5: note: in expansion of macro ‘bam_seek’
     bam_seek(fp, 0, 0);
     ^~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c io_sam.c -o io_sam.o
In file included from /home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/sam.h:29:0,
                 from io_sam.c:2:
io_sam.c: In function ‘_scan_bam_all’:
/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:5: note: in expansion of macro ‘bam_seek’
     bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
     ^~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pileup.cpp -o pileup.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c pileupbam.c -o pileupbam.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sam.c -o sam.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sam_opts.c -o sam_opts.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c sam_utils.c -o sam_utils.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c samtools_patch.c -o samtools_patch.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c scan_bam_data.c -o scan_bam_data.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tabixfile.c -o tabixfile.o
tabixfile.c: In function ‘index_tabix’:
tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
     if (bgzf_is_bgzf(fn) != 1)
     ^~
In file included from tabixfile.c:3:0:
/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
         ^~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c tagfilter.c -o tagfilter.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c utilities.c -o utilities.o
gcc -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/S4Vectors/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/IRanges/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/XVector/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/Biostrings/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c zip_compression.c -o zip_compression.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /home/biocbuild/bbs-3.11-bioc/R/library/Rhtslib/usrlib/libhts.a -lcurl -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-Rsamtools/00new/Rsamtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rsamtools)

Tests output

Rsamtools.Rcheck/tests/Rsamtools_unit_tests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage('Rsamtools')

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

[E::COMPAT_bcf_hdr_read] Input is not detected as bcf or vcf format
[E::hts_idx_push] Chromosome blocks not continuous
[E::hts_open_format] Failed to open file http://httpbin.org/status/504


RUNIT TEST PROTOCOL -- Sat Oct 17 05:04:35 2020 
*********************************************** 
Number of test functions: 180 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
Rsamtools RUnit Tests - 180 test functions, 0 errors, 0 failures
Number of test functions: 180 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
2: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
3: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
4: In read.table(conn, colClasses = colClasses, col.names = names(colClasses),  :
  not all columns named in 'colClasses' exist
> 
> proc.time()
   user  system elapsed 
 19.673   1.021  21.508

Example timings

Rsamtools.Rcheck/Rsamtools-Ex.timings

nameusersystemelapsed
ApplyPileupsParam-class0.0260.0000.026
BamFile-class0.4050.0120.417
BamViews-class0.0470.0000.047
BcfFile-class0.1980.0040.219
FaFile-class0.0520.0000.053
PileupFiles-class0.0090.0000.009
Rsamtools-package0.0090.0000.009
ScanBamParam-class0.5860.0080.594
ScanBcfParam-class000
TabixFile-class0.0300.0080.038
applyPileups000
headerTabix0.0030.0000.003
indexTabix0.0400.0000.051
pileup38.275 0.10438.383
quickBamFlagSummary0.0260.0000.026
readPileup0.0820.0030.218
scanBam0.7890.0210.809
scanBcf0.4970.0000.496
scanFa0.0650.0000.066
scanTabix0.0680.0000.067
seqnamesTabix0.0040.0000.004
testPairedEndBam0.0240.0000.025
zip0.0310.0000.030